GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Phyllobacterium endophyticum PEPV15

Align candidate WP_106714834.1 CU100_RS01740 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00263.hmm
# target sequence database:        /tmp/gapView.177507.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00263  [M=385]
Accession:   TIGR00263
Description: trpB: tryptophan synthase, beta subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-192  623.5   0.0   8.7e-192  623.3   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106714834.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106714834.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.3   0.0  8.7e-192  8.7e-192       1     383 [.      18     410 ..      18     412 .. 0.97

  Alignments for each domain:
  == domain 1  score: 623.3 bits;  conditional E-value: 8.7e-192
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskkl.......... 63 
                                           g+fg fGG++v+e+l++ + el++ay++ak+d++fk+el+ l  +yagrp+ l++a+ l++++          
  NCBI__GCF_003010935.1:WP_106714834.1  18 GMFGIFGGRFVAETLMPLILELQQAYDDAKNDPAFKAELQALSTHYAGRPSKLYYAEGLTRHVrqlareqgld 90 
                                           79*******************************************************9998753333333344 PP

                             TIGR00263  64 ggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedver 136
                                           ggakiy+kredl+htG+hkinn lgq+lla+r+Gk+riiaetGaGqhGva+at++a++gl c+vymGa+dver
  NCBI__GCF_003010935.1:WP_106714834.1  91 GGAKIYFKREDLNHTGSHKINNCLGQILLARRMGKTRIIAETGAGQHGVASATVSARFGLPCVVYMGATDVER 163
                                           579********************************************************************** PP

                             TIGR00263 137 qklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevke 209
                                           qk+nvfrm+llga+v+pv+sG+ tlkda+nealrdWv++vedt+y++G+a+GphP+Pe+vr+fq+vig+e++e
  NCBI__GCF_003010935.1:WP_106714834.1 164 QKPNVFRMKLLGAEVKPVSSGHGTLKDAMNEALRDWVSNVEDTYYLIGTAAGPHPYPEMVRDFQAVIGTEARE 236
                                           ************************************************************************* PP

                             TIGR00263 210 qilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkll 282
                                           qile+egrlPd+++a+vGGGsnaiG+f++f++d +ve+ig+eagG+G+d e+h+a++s+G++GvlhG++t+ll
  NCBI__GCF_003010935.1:WP_106714834.1 237 QILEREGRLPDTIVAAVGGGSNAIGLFHPFLDDRQVEIIGIEAGGRGLDGEEHCASMSAGRPGVLHGNRTYLL 309
                                           ************************************************************************* PP

                             TIGR00263 283 qdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaalek 355
                                           q++dGqi + hsvsaGldypgvgPeh++l +tgr++y+ + d+eal+a++l +++eGiipales+ha+a+++k
  NCBI__GCF_003010935.1:WP_106714834.1 310 QNKDGQILDGHSVSAGLDYPGVGPEHSWLRDTGRVSYVPVLDNEALDAFTLTTRTEGIIPALESAHAIAHAVK 382
                                           ************************************************************************* PP

                             TIGR00263 356 lapklkkdeivvvnlsGrGdkdletvak 383
                                           +apk+++d+i++vnlsGrGdkd++tv +
  NCBI__GCF_003010935.1:WP_106714834.1 383 IAPKMAQDKIMIVNLSGRGDKDVHTVGQ 410
                                           ************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (416 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.47
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory